datatable(pro_summs2, rownames = FALSE, filter="top", options = list(pageLength = 5, scrollX=T) )
mu2 <- mus[[2]]
datatable(mu2, rownames = FALSE, filter="top", options = list(pageLength = 5, scrollX=T) )
mu3 <- mus[[3]]
datatable(mu3, rownames = FALSE, filter="top", options = list(pageLength = 5, scrollX=T) )
grid.raster(readPNG("figures/ssc_probands_phe.png"))
grid.raster(readPNG("figures/ssc_unaffSibs_phe.png"))
grid.raster(readPNG("figures/ssc_otherSibs_phe.png"))
sex <- read.table("../outputs/sexcheck.txt", header = T, stringsAsFactors = F)
res_sex1 <- sex[sex$chip == "UCSF_1Mv3",]
res_sex2 <- sex[sex$chip == "UCSF_1Mv1",]
res_sex3 <- sex[sex$chip == "UCSF_Omni2.5",]
fams <- read.table("../outputs/fams_covarites.txt", stringsAsFactors = F)
fam1 <- fams[fams$V7 == "1Mv3",]
fam2 <- fams[fams$V7 == "1Mv1",]
fam3 <- fams[fams$V7 == "Omni2.5",]
##confirm with other phenotype file
pros <- sex[sex$STATUS == "PROBLEM",]
pros$RRB <- "NA"
pros[pros$IID %in% fams$V2,]$RRB <- fams[match(pros[pros$IID %in% fams$V2,]$IID, fams$V2), "V8"]
datatable(pros, rownames = FALSE, filter="top", caption = htmltools::tags$caption(
style = 'caption-side: top; text-align: center; color:black;
font-size:200% ;',"Individuals with discordant sex information"), options = list(pageLength = 5, scrollX=T) )
grid.raster(readPNG("figures/sex_1mv3.png"))
grid.raster(readPNG("figures/sex_1mv1.png"))
grid.raster(readPNG("figures/sex_omni.png"))
grid.raster(readPNG("figures/ibd_1mv3.png"))
grid.raster(readPNG("figures/ibd_1mv1.png"))
grid.raster(readPNG("figures/ibd_omni.png"))
grid.raster(readPNG("figures/ibd_sexF_1mv3.png"))
grid.raster(readPNG("figures/ibd_sexF_1mv1.png"))
grid.raster(readPNG("figures/ibd_sexF_omni.png"))
grid.raster(readPNG("figures/p_het.png"))
grid.raster(readPNG("figures/p_F.png"))
grid.raster(readPNG("figures/p_het_ibd1.png"))
grid.raster(readPNG("figures/p_het_ibd2.png"))
grid.raster(readPNG("figures/p_het_ibd3.png"))